1wnz
From Proteopedia
(New page: 200px<br /><applet load="1wnz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wnz, resolution 1.70Å" /> '''Isoleucyl-tRNA synth...) |
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| - | [[Image:1wnz.gif|left|200px]]<br /><applet load="1wnz" size=" | + | [[Image:1wnz.gif|left|200px]]<br /><applet load="1wnz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wnz, resolution 1.70Å" /> | caption="1wnz, resolution 1.70Å" /> | ||
'''Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA'''<br /> | '''Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to | + | In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In the present study, we determined the crystal structures of the Thermus thermophilus IleRS editing domain complexed with the substrate analogues in the pre and post-transfer modes, both at 1.7 A resolution. The active site accommodates the two analogues differently, with the valine side-chain rotated by about 120 degrees and the adenosine moiety oriented upside down. The substrate-binding pocket adjusts to the adenosine-monophosphate and adenosine moieties in the pre and post-transfer modes, respectively, by flipping the Trp227 side-chain by about 180 degrees . The substrate recognition mechanisms of IleRS are characterized by the active-site rearrangement between the two editing modes, and therefore differ from those of the homologous valyl and leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer mode is predominant. Both modes of editing activities were reduced by replacements of Trp227 with Ala, Val, Leu, and His, but not by those with Phe and Tyr, indicating that the aromatic ring of Trp227 is important for the substrate recognition. In both editing modes, Thr233 and His319 recognize the substrate valine side-chain, regardless of the valine side-chain rotation, and reject the isoleucine side-chain. The T233A and H319A mutants have detectable editing activities against the cognate isoleucine. |
==About this Structure== | ==About this Structure== | ||
| - | 1WNZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with 2VA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] Full crystallographic information is available from [http:// | + | 1WNZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=2VA:'>2VA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
[[Category: Fukunaga, R.]] | [[Category: Fukunaga, R.]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
[[Category: 2VA]] | [[Category: 2VA]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:46:26 2008'' |
Revision as of 13:46, 21 February 2008
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Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA
Overview
In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In the present study, we determined the crystal structures of the Thermus thermophilus IleRS editing domain complexed with the substrate analogues in the pre and post-transfer modes, both at 1.7 A resolution. The active site accommodates the two analogues differently, with the valine side-chain rotated by about 120 degrees and the adenosine moiety oriented upside down. The substrate-binding pocket adjusts to the adenosine-monophosphate and adenosine moieties in the pre and post-transfer modes, respectively, by flipping the Trp227 side-chain by about 180 degrees . The substrate recognition mechanisms of IleRS are characterized by the active-site rearrangement between the two editing modes, and therefore differ from those of the homologous valyl and leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer mode is predominant. Both modes of editing activities were reduced by replacements of Trp227 with Ala, Val, Leu, and His, but not by those with Phe and Tyr, indicating that the aromatic ring of Trp227 is important for the substrate recognition. In both editing modes, Thr233 and His319 recognize the substrate valine side-chain, regardless of the valine side-chain rotation, and reject the isoleucine side-chain. The T233A and H319A mutants have detectable editing activities against the cognate isoleucine.
About this Structure
1WNZ is a Single protein structure of sequence from Thermus thermophilus with as ligand. Active as Isoleucine--tRNA ligase, with EC number 6.1.1.5 Full crystallographic information is available from OCA.
Reference
Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase., Fukunaga R, Yokoyama S, J Mol Biol. 2006 Jun 16;359(4):901-12. Epub 2006 Apr 25. PMID:16697013
Page seeded by OCA on Thu Feb 21 15:46:26 2008
Categories: Isoleucine--tRNA ligase | Single protein | Thermus thermophilus | Fukunaga, R. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Yokoyama, S. | 2VA | Ligase | National project on protein structural and functional analyses | Nppsfa | Riken structural genomics/proteomics initiative | Rsgi | Structural genomics
